Merge d072f1c into 8b65889

notebooks/numpy_differences.ipynb

@@ -0,0 +1,121 @@
+{
+ "metadata": {
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.6.9-final"
+  },
+  "orig_nbformat": 2,
+  "kernelspec": {
+   "name": "python_defaultSpec_1600360623664",
+   "display_name": "Python 3.6.9 64-bit ('.venv': virtualenv)"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2,
+ "cells": [
+  {
+   "source": [
+    "# Numpy version\n",
+    "\n",
+    "Numpy version >1.19 makes some ever so small changes to the test data making them not pass. It appears to be the vapor pressure from HRRR because the air temperature is fine but not variables derived from vapor pressure like precip temperature and thermal.\n",
+    "\n",
+    "- air temperature is exactly the same from HRRR\n",
+    "- relative humidity is exactly the same from HRRR\n",
+    "- vapor pressure is float noise\n"
+   ],
+   "cell_type": "markdown",
+   "metadata": {}
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import pandas as pd\n",
+    "import numpy as np"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [
+    {
+     "output_type": "execute_result",
+     "data": {
+      "text/plain": "array([0.])"
+     },
+     "metadata": {},
+     "execution_count": 2
+    }
+   ],
+   "source": [
+    "# air temperature\n",
+    "old = pd.read_csv('../ta_old.csv', parse_dates=True, index_col='date_time')\n",
+    "new = pd.read_csv('../ta_new.csv', parse_dates=True, index_col='date_time')\n",
+    "d = old - new\n",
+    "np.unique(d)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "output_type": "execute_result",
+     "data": {
+      "text/plain": "array([0.])"
+     },
+     "metadata": {},
+     "execution_count": 3
+    }
+   ],
+   "source": [
+    "# relative humidity\n",
+    "old = pd.read_csv('../rh_old.csv', parse_dates=True, index_col='date_time')\n",
+    "new = pd.read_csv('../rh_new.csv', parse_dates=True, index_col='date_time')\n",
+    "d = old - new\n",
+    "np.unique(d)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "output_type": "execute_result",
+     "data": {
+      "text/plain": "array([-2.11303719e-04, -2.09472666e-04, -7.00683595e-05, -6.70166046e-05,\n       -5.78613290e-05, -1.80358875e-05,  0.00000000e+00,  1.29699711e-04,\n        1.82006839e-04,  1.91406260e-04])"
+     },
+     "metadata": {},
+     "execution_count": 4
+    }
+   ],
+   "source": [
+    "# vapor pressure\n",
+    "old = pd.read_csv('../vp_old.csv', parse_dates=True, index_col='date_time')\n",
+    "new = pd.read_csv('../vp_new.csv', parse_dates=True, index_col='date_time')\n",
+    "d = old - new\n",
+    "np.unique(d)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ]
+}

requirements.txt

@@ -1,8 +1,7 @@
 coloredlogs
-Cython>=0.28.4
 inicheck>=0.9.0,<0.10.0
 netCDF4>=1.2.9
-numpy>=1.14.0,<1.19.0
+numpy>=1.14.0
 pandas>=0.23.0
 pytz==2017.3
 scipy>=1.0.0,<1.5.0

requirements_dev.txt

@@ -1,4 +1,5 @@
 -r requirements.txt
+Cython
 coveralls>=1.3.0
 tox>=3.14.0
 flake8>=3.5.0
@@ -9,4 +10,4 @@ pydata-sphinx-theme
 sphinxcontrib-bibtex>=1.0
 sphinxcontrib-websupport>=1.0.1
 pygit2
-git+https://github.com/USDA-ARS-NWRC/goldmeister.git@master
+git+https://github.com/USDA-ARS-NWRC/goldmeister.git@main

setup.py

@@ -3,30 +3,40 @@
 
 import os
 
-import numpy
-from Cython.Distutils import build_ext
 from setuptools import Extension, find_packages, setup
+from setuptools.command.build_ext import build_ext as _build_ext
+
+# Test if compiling with cython or using the C source
+try:
+    from Cython.Distutils import build_ext as _build_ext
+except ImportError:
+    USE_CYTHON = False
+else:
+    USE_CYTHON = True
+
+print('Using Cython {}'.format(USE_CYTHON))
+ext = '.pyx' if USE_CYTHON else '.c'
 
 
 def c_name_from_path(location, name):
     return os.path.join(location, name).replace('/', '.')
 
 
-with open('requirements.txt') as requirements_file:
-    requirements = requirements_file.read()
+class build_ext(_build_ext):
+    def finalize_options(self):
+        _build_ext.finalize_options(self)
+        # Prevent numpy from thinking it is still in its setup process:
+        __builtins__.__NUMPY_SETUP__ = False
+        import numpy
+        self.include_dirs.append(numpy.get_include())
 
-with open('README.md') as readme_file:
-    readme = readme_file.read()
 
 # Give user option to specify his local compiler name
 if "CC" not in os.environ:
-    # force the compiler to use gcc
     os.environ["CC"] = "gcc"
 
-
 ext_modules = []
 extension_params = dict(
-    include_dirs=[numpy.get_include()],
     extra_compile_args=['-fopenmp', '-O3'],
     extra_link_args=['-fopenmp', '-O3'],
 )
@@ -37,7 +47,7 @@ def c_name_from_path(location, name):
     Extension(
         c_name_from_path(source_folder, 'detrended_kriging'),
         sources=[os.path.join(source_folder, val) for val in [
-            "detrended_kriging.pyx",
+            "detrended_kriging" + ext,
             "krige.c",
             "lusolv.c",
             "array.c"
@@ -52,7 +62,7 @@ def c_name_from_path(location, name):
     Extension(
         c_name_from_path(source_folder, 'envphys_c'),
         sources=[os.path.join(source_folder, val) for val in [
-            "envphys_c.pyx",
+            "envphys_c" + ext,
             "topotherm.c",
             "dewpt.c",
             "iwbt.c"
@@ -67,14 +77,24 @@ def c_name_from_path(location, name):
     Extension(
         c_name_from_path(source_folder, 'wind_c'),
         sources=[os.path.join(source_folder, val) for val in [
-            "wind_c.pyx",
+            "wind_c" + ext,
             "breshen.c",
             "calc_wind.c"
         ]],
         **extension_params
     ),
 ]
 
+cmdclass = {}
+if USE_CYTHON:
+    cmdclass = {'build_ext': build_ext}
+
+with open('requirements.txt') as requirements_file:
+    requirements = requirements_file.read()
+
+with open('README.md') as readme_file:
+    readme = readme_file.read()
+
 setup(
     name='smrf-dev',
     description="Distributed snow modeling for water resources",
@@ -110,9 +130,7 @@ def c_name_from_path(location, name):
     ],
     test_suite='smrf.tests',
     # tests_require=test_requirements,
-    cmdclass={
-        'build_ext': build_ext
-    },
+    cmdclass=cmdclass,
     ext_modules=ext_modules,
     scripts=[
         'scripts/update_configs',
@@ -130,6 +148,7 @@ def c_name_from_path(location, name):
         'local_scheme': 'node-and-date',
     },
     setup_requires=[
-        'setuptools_scm'
+        'setuptools_scm',
+        'numpy'
     ],
 )